https://github.com/databio/lolahema_pep

Portable Encapsulated Project for the LOLAHema database.
https://github.com/databio/lolahema_pep

Last synced: 2 months ago
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Portable Encapsulated Project for the LOLAHema database.

• Host: GitHub
• URL: https://github.com/databio/lolahema_pep
• Owner: databio
• Created: 2019-10-21T19:34:47.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2021-10-09T22:57:56.000Z (over 4 years ago)
• Last Synced: 2025-09-11T10:15:38.781Z (10 months ago)
• Language: R
• Size: 167 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

          
# LOLAHema_PEP

Portable Encapsulated Project (PEP) for the LOLAHema database.  

This [PEP](http://pep.databio.org/en/latest/) is specifically designed to encompass public AML relevant samples. The PEP sample sheet and config files can be accessed directly with the following links:

- [Sample sheet](https://github.com/databio/LOLAHema_PEP/blob/master/LOLAHema_samples.csv)

- [YAML Config file](https://github.com/databio/LOLAHema_PEP/blob/master/LOLAHema_samples_cfg.yaml) 

The .csv sample sheet contains the following attributes for each of the files:  

- **sample_name**

- **file_name**

- **genome**

- **experimental protocol**

- cell type

- tissue

- antibody

- treatment

- data_source

- GSE

- GSM

- description

- file format

The attributes highlighted in bold are used to create derived attributes such as `output_file_path` which points to the location of the BED files produced by the [bedmaker](https://github.com/databio/bedmaker) pipeline (please take a look at the config file). Accordingly, samples in this PEP can be easily processed with other PEP compatible pipelines such as [bedstat](https://github.com/databio/bedstat) and [bedbuncher](https://github.com/databio/bedbuncher). 

There is an additional PEP ([lifOver_PEP](https://github.com/databio/LOLAHema_PEP/tree/master/liftOver_PEPs)) in the repository that contains files that have been liftedOver to different reference genome assemblies (e.g., hg19 to hg38).